Re: Using org-mode for laboratory notes.

[Eric Lubeck <eric.lubeck@gmail.com>]

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Hey, 

Thanks for the good idea.  I'll have to look into figuring that system out.

On the broader point of organizing the notebook, I am still having a bit of a dilemma coming up with an effective system.  My first thought was to just place all my work in a dated hierarchy, such as with org-datetree.  This would be simple and mirror a conventional notebook, but would loose a lot of the logical hierarchy possible with digital tools.  

On the other hand, organizing all my experiments as a non-linear outline is getting a bit messy.  I found myself navigating around headlines everyday searching for items I need to schedule for the next day.  As my notebook gets bigger, this system will probably get very inefficient.  If i properly tag and schedule my tasks for the day this should be less of a problem, but i still foresee potential chaos if I get lazy.  In addition to tasks I intend to record other observations in the notebook that may not be associated with a recent task, yet are important for me planning future experiments.  Without proper timestamps I could loose these observations over time.

This is where I came up with the idea of tagging all of my headlines with their entry date and timestamp.  Potentially such a system would enable me to view the logical hierarchy of an experiment, but also view my work in the conventional linear order. 

Anyone have any other ideas for reasonable systems?

I'm also a bit confused about the proper way to implement such a system.  I imagine I could hack together some auto-timestamp property, but than it would only apply to headlines, not to my nested observations in list form.  For this reason I have little used lists at all in org-mode, as it seems that any data that could potentially be nested, such as with different tasks or properties, must be converted back to headline form before it can be annotated.  Am I missing something?

Also, I have a general question about nesting headings demonstrated by the below example.

* Today's Experiment       :EXPERIMENT:
** Do today's Experiment :RATIONALE:
** Data link :DATA:
** Experiments are sad.  :DISCUSSION:
** Repeat, but change X <Tomorrow>  :FOLLOW-UP:
* Tomorrow's Experiment  :EXPERIMENT:
** <Yesterday's Experiment> Failed :RATIONALE:
*** Determine if X was the cause

In the above case I have two options, to either continually nest all follow-up experiments, or rely on a network of links to get me back to the data that led to the follow-up experiments.  Anybody have any advice on pursing either option?

Thanks for the help,
Eric Lubeck


On Wednesday, September 19, 2012 at 6:44 PM, Torsten Wagner wrote:

> Hi,
> 
> one way which works rather differently is the combination of git and org-mode.
> You could write your protocols in separate org-files and link to them
> in your records.
> org allows (at least it did a while ago) to link not only to a file
> but also to a specific version of a file.
> You could do small modification in the protocol-files as you need them
> and check them into the git system.
> Link to them and you will see the version you used for exactly this experiments.
> 
> Actually using something like git and a git sensitive link is
> important if you might plan link to a lot of external files. Imaging
> you overwrite a file by accident or because you can't remember you
> referred to the original file already. A normal link would quietly
> point to the new file and would not be in-sync with anything you
> mentioned in your org-file.
> 
> Other benefits are gits diff, merge and change-recording capabilities.
> If you set-up the git repro with entire lab-book on a server (a PC
> reachable from all your other devices) you could easily add data from
> within the lab, go to your office to add more data and at a certain
> point merge all this together. Both PCs could work offline and only
> need to be online for check-in and check-out new data.
> Another benefit of combining org-mode and git... you can tag certain
> versions of your lab book. E.g. tag them whenever you write a paper
> and make a notice in org-mode. This enables you to get back to all the
> measurement and reps. data evaluation results as you found them during
> writing your paper, even years and many many changes later (e.g. you
> might improved your data analysis method over time but for the paper
> you still want to see the old stupid way how you dealt with the data).
> 
> Recently we got an org-file sensitive git-module, which makes merging
> org-files much more nice.
> Check here:
> 
> http://orgmode.org/worg/org-contrib/org-git-link.html
> http://orgmode.org/worg/org-contrib/gsoc2012/student-projects/git-merge-tool/index.html
> 
> Albeit I have to say I like to do all kind of stuff in org-mode, I
> faced problems using only org-mode as lab-notebook. Sometimes things
> in a lab are to numerous and to verbose to type them all in as they
> happen. Sometimes a little sketch, some quick scribbled note, etc.
> contains the real important data.... sentences like "Damn, Joe slammed
> the door AGAIN", during an AFM measurement. Or in your case "Uhh..
> what are the funny little flakes in my buffer solutions".... I think
> sometimes a keyboard still filters to much and hence org-mode might
> not really contain all the necessary info.
> As a summary:
> org-mode as a lab-book will work fine if you are strict in using it
> and force yourself to be verbose enough.
> 
> Hope thats helps
> 
> Totti
> 
> CC. There might be some legal issue with real lab books and electronic
> once. Back in the good old time where scientists didn't publish each
> and every result and where it could take many many months until some
> discovery reached the other side of the planet, the laboratory books
> where the legal evidence of the original work. If someone made a wrong
> claim or someone accused someone else of falsify reporting, the
> laboratory books where used to proof those claims. That is the reason,
> you find e.g. nicely archived laboratory books of all the great
> scientists of the Bell laboratories. Not sure how much this is still
> relevant today.
> 
> 
> On 20 September 2012 03:49, Eric Schulte <eric.schulte@gmx.com (mailto:eric.schulte@gmx.com)> wrote:
> > Eric Lubeck <eric.lubeck@gmail.com (mailto:eric.lubeck@gmail.com)> writes:
> > 
> > > Hello Everybody,
> > > 
> > > I had a look around the web for awhile, but couldn't find any
> > > information pertaining to my particular needs. I hope somebody here
> > > will be able to help me out.
> > > 
> > > Anyway, I've been looking around for quite a while for the proper
> > > system to set-up an electronic laboratory notebook in. I will be
> > > using org-mode to document wet-lab experiments in addition to
> > > computational work.
> > > 
> > > One of my particular concerns is this: I'm accustomed to using a
> > > chronological laboratory notebook for recording all of my data. The
> > > agenda views in org-mode seem to provide a means to retrieve
> > > chronological information out of my outlines, but I would than need to
> > > timestamp every single entry in my outline. Is there a means for
> > > doing this? Currently I am manually typing C-u C-c ! , but it would
> > > be helpful to have something automatically configured to timestamp and
> > > place the time in a drawer for any entry in a particular file.
> > > 
> > 
> > 
> > I believe such automated functionality may exist (although I don't use
> > it personally). Take a look at this portion of the manual [1].
> > 
> > > 
> > > My other question pertains to efficiently representing linked or
> > > nested data. I'd like to record my detailed laboratory protocols in
> > > another outline. As most of my day-to-day work is using these
> > > protocols with minimal modifications, I'd like to record in my primary
> > > outline a property or hyperlink that points to the primary protocol
> > > and suggests that this days experiment "inherits" from the main
> > > protocol with given modifications. It would be really awesome if the
> > > protocol tree could than pick up on these distant inheriting protocols
> > > and transclude in the dates I have performed this protocol and
> > > subsequent modifications from the "lab notebook" section. Is such a
> > > task possible with org-mode, or must I look towards a more traditional
> > > database?
> > > 
> > 
> > 
> > If I read this paragraph correctly, you want to be able to collect the
> > dates from every entry in which a particular protocol was used. If you
> > assign each protocol a short tag name, then you could tag each daily
> > experiment with the date and the protocol used. Armed with your tagged
> > headlines Org-mode should provide everything required to search for and
> > collect your experiments based on tags, and to do things like collect
> > the dates on which each tag was used. Look at the tag and searching
> > sections of the Org-mode manual [2], and maybe look at the org-collector
> > in the contrib portion of Worg [3].
> > 
> > > 
> > > Thanks,
> > > Eric Lubeck
> > > 
> > 
> > 
> > 
> > Footnotes:
> > [1] http://orgmode.org/manual/Clocking-work-time.html
> > 
> > [2] http://orgmode.org/manual/Tags.html
> > 
> > [3] http://orgmode.org/worg/org-contrib/org-collector.html
> > 
> > --
> > Eric Schulte
> > http://cs.unm.edu/~eschulte
> > 
> 
> 
> 



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